Adding percentage assay

[daramirez]

Adding a new assay with the percentage of cells with counts > 0 per gene per keyfield.

[GWMcElfresh]

Somehow this broke the merge step in RunFilteredContrasts:

Before:

[1] "Layers: counts.1,counts.2,data.1,scale.data.1,data.2,scale.data.2"
[1] "Class: Assay5"
[1] "Joining layers: RNA"
[1] "After join: scale.data,data,counts"
[1] "Remaining Cells:" "8"               
[1] "colsums: 8"
[1] "Performing DE for:  unvax_baseline-vaccineOne_baseline"

After:

[1] "Layers: counts.1,counts.2,data.1,scale.data.1,data.2,scale.data.2"
[1] "Class: Assay5"
[1] "Joining layers: RNA"
[1] "After join: scale.data,data,counts"
[1] "Remaining layers: scale.data,data,counts"
[1] "Error subsetting in contrast: unvax_baseline-vaccineOne_baseline. Column:timepoint"
[1] "Error: Error in MergeSplitLayers(seuratObj.contrast): Layers were not joined!\n"

It's probable that I coded up some assumption that breaks when there's a second assay present or merge doesn't know what to do with incompatible counts layers.

[GWMcElfresh]

RunFilteredContrasts doesn't return a seurat object and asks for a specific assayName argument, so I opted to remove any unspecified assays, which fixes this locally.